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iii, Materials Studio Online Help Tutorials.,. Accelrys Basic Training, Materials Studio,., Online Help,., Materials Studio,,.., Web http://accelrys.co.jp/.,,.,,,. : support-japan@accelrys.com : 03-5532-3860 : 03-5532-3802 ( : 10:00 17:00,, ), Web FAQ (http://accelrys.co.jp/customer-support/faq.html),,. FAQ. Username: faq Password: accelryskk Version 1.3 c 2010.,,.

v 1 DMol 3........................... 1 1.1.............................................. 2 1.2 DMol 3...................................... 2 1.3............................. 4 1.4...................................... 5 1.5 DOS PDOS.................................... 7 2 DMol 3................................. 9 2.1.............................................. 10 2.2 DMol 3...................................... 10 2.3............................. 13 2.4.......................................... 14 3 LST/QST............................. 21 3.1.............................................. 22 3.2.................................. 22 3.3........................................ 24 3.4................................... 25 3.5 LST/QST/CG......................... 27 3.6............................... 28 3.7 LST/QST.................................. 29 4.................................. 33 4.1.............................................. 34 4.2.................................. 34 4.3................................. 36 4.4......................... 37 5 (Coumarin).............................. 41 5.1.............................................. 41 5.2.................................. 42 5.3........................ 43 5.4......................... 43 A..................................... 45

1 1 DMol 3 :. : Materials Visualizer, DMol 3 :.,,.,,,,,.,. (density of states, DOS). DOS., DOS, DOS 1, 0.,, DOS. DOS,., (PDOS), (s, p, d, or f)., DMol 3,, DOS, PDOS.. DMol 3 DOS PDOS Note., Setting Organizer. Creating a project. Tip.. Project Explorer, Online Help Project Explorer.

2 1.1 Materials Studio,. New Project, AlAs DOS OK., AlAs DOS, Project Explorer.. Materials Studio,.,. File Import..., Import Document. Structures/semiconductors/AlAs.msi, Open. AlAs. 3D Viewer,. 1.2 DMol 3, 8, 2.,,,.,. Build Symmetry Primitive Cell. 1: The primitive cell of AlAs DMol3, Calculation, Modules DMol3 Calculation. DMol3 Calculation.

3 2: DMol3 Calculation dialog, Setup tab Task Energy. Functional LDA PWC, Quality Medium. Medium,. Properties.. 3: DMol3 Calculation dialog, Properties tab Band structure.

4 Empty bands 12, k-point set Medium., k-point set. Path..., Brillouin Zone Path. Create. Reset,. 4: Brillouin Zone Path dialog 3D Viewer,,, Brillouin Zone Path k..., [0.5, 0.25, 0.75] [0.5, 0.5, 0.5].,.,., W [0.5, 0.25, 0.75], Γ G, [0, 0, 0]. Brillouin Zone Path,,. Properties k-point set,.,. DMol3 Calculation. Properties Density of states, (PDOS), Calculate PDOS. 1.3 Job Control DMol 3. DMol3 Calculation Job Control. Job Control.

5 5: DMol3 Calculation dialog, Job Control tab,,. More... DMol3 Job Control Options,. live update,. DMol 3. Run. Job Explorer,. Status.txt.. 1.4, Project Explorer AlAs DMol3 Energy. AlAs DMol3 Energy AlAs.xtd. AlAs 3D model..,. DMol3, Analysis, Modules DMol3 Analysis. DMol3 Analysis.

6 6: DMol3 Analysis dialog, Band structure selection Band structure, View.. 7: DMol 3 band structure for AlAs. Γ (G) 0.1 Hartree (2.7 ev),., 1., AlAs 0.054 Ha (1.5 ev), 1 r,.

7 (2.2 ev).,. 1.5 DOS PDOS AlAs DMol3 Energy AlAs.xsd. DMol3 Analysis Density of states. Partial, s, p, d, Sum. More..., Integration method Interpolation OK. View. PDOS. 8: PDOS for AlAs Tip. Integration method Smearing,,., Fermi,., Inerpolation,, k. (Energy = 0 Ha).,,,.. s, p, d., (LDOS).

8 AlAs DMol3 Energy AlAs.xsd. Al. (Al. ), PDOS. As PDOS. Al As,. File Save Project, Window Close All. 9: LDOS of As 10: LDOS of As.

9 2 DMol 3 :. : Materials Visualizer, DMol 3 : DMol 3,. Materials Studio DMol 3.,.,, 2-5. DMol 3,.. DMol 3 Note., Setting Organizer. Creating a project. Tip.. Project Explorer, Online Help Project Explorer.

10 2.1 Materials Studio,. New Project, Chabazite OK., Chabazite, Project Explorer.,. Materials Studio,. (chabazite). File Import..., Import Document. Examples/Documents/3D Model/CHA.xsd, Open. 3D Viewer, Display Style, Display Style. Polyhedron,. CHA 3D Viewer. 11: A unit cell of chabazite 2.2 DMol 3 DMol3. Calculation, Modules DMol3 Calculation DMol3 Calculation.

11 12: DMol3 Calculation dialog, Setup tab Task Geometry Optimization. Quality Medium. Funcitonal LDA, VWN. Medium, Quality basis set integration grid convergence thresholds. More..., DMol3 Geometry Optimization. 13: DMol3 Geometry Optimization dialog Convergence tolerance Quality,,. Medium.,.

12 Quality Medium,. DMol3 Calculation Electronic. DMol3 Calculation Electronic.. 14: DMol3 Calculation dialog, Electronic tab,., k-point set Orbital cutoff quality. k-point set Gamma, Orbital cutoff quality Coarse. More..., DMol3 Electronic Options. Orbital Cutoff orbital cutoff 3.5 Å.. DMol3 Calculation Electronic Orbital cutoff quality. DMol3 Electronic Options. Tip. DMol3 Electronic Options, SCF k-point. DMol3 Calculation Properties. Properties,.

13 15: DMol3 Calculation dialog, Properties tab Electron density Electrostatics. 2.3 Job Control DMol 3. DMol3 Calculation Job Control. Job Control. 16: DMol3 Calculation dialog, Job Control tab,,. More... DMol3 Job Control Options

14,. live update,. DMol 3. Run. Job Explorer,. Status.txt..,, CHA Energies.xcd CHA Convergence.xcd 2.. 2.4, Project Explorer CHA DMol3 GeomOpt. CHA DMol3 GeomOpt CHA.xtd. CHA 3D model.,. Animation., Animation, View Toolbars Animation. Animation Play,., Stop,. Tip. Animation Mode, Options, Animation Options.,,..outmol. CHA.outmol. total energy..xsd. Project Explorer CHA DMol3 GeomOpt CHA.xsd.,. DMol3., Analysis, Modules DMol3 Analysis DMol3 Analysis.

15 Electron density, Results.outmol. Density field Total density, View isofurface on import. Import.. 17: Electron density of CHA. (isosurface),,. Display Style, Atom Stick., Isosurface. Transparency,., Dots Solid.

16 18: Display Style dialog Transparency,.. Isovalule 0.1 Tab. 0.2, Tab.,. DMol3 Analysis Potentials, View isosurface on import. Import. Display Style Isosurface, Mapped field DMol3 electrostatic potential,.. Color Map,.

17 19: Electron density and electrostatic potential of CHA 3D Viewer Color Maps. Color Maps.. 20: Color Maps dialog Spectrum Blue-White-Red. From, Mapped Minimum. To, Mapped Maxiumum,.,. Volume Visualization,. View Toolbars Volume Visualization. Volume Visulization.,,. Create Slices, Best Fit, Choose Fields to Slice. DMol3 electrostatic potential, OK.

18 21: Choose Fields to Slice dialog.. 22: Electron density and electrostatic potential of CHA, Color Maps. Color Maps,.,,. From, Mapped Minimum. To, Mapped Mean. Spectrum Blue-White-Red.

19 23: Electron density and electrostatic potential of CHA,, Mapped Maximum Mapped Mean. Color Maps,...,.,. Color Maps. Display Style Slice. Display Style. Slice, Transparency. Transparency,., Delete, 3D Viewer., Delete.., Online Help Creating and customizing slices. File Save Project, Window Close All.

20.

21 3 LST/QST : DMol 3 Reaction Preview. : Materials Visualizer, DMol 3 :,.,,.,, Linear Synchronous Transit (LST) Quadratic Synchronous Transit (QST). DMol3 LST/QST. LST/QST. CH 2 CHOH CH 3 COH (1). LST/QST/CG Note.,. Note., Setting Organizer. Creating a project.

22 Tip.. Project Explorer, Online Help Project Explorer. 3.1 Materials Studio,. New Project, vinyloh OK., vinyloh, Project Explorer. 3.2, 2 3D Atomistic. 3D Atomistic,. New, 3D Atomistic Document. Sketch, 3. Esc. Shift 2,. Modify Elements, Oxygen... Ctrl,. Shift 1. Modify Bond Order, Double Bond., Ctrl,. Adjust Hydrogens, Clean.,. ( ). 2 Skecth Shift, Ctrl, 3D Viewer Selection Mode.

23 24: The sturucture of vinyl alcohol Project Explorer 3D Atomistic.xsd, Rename. reactant, Enter. 3D Viewer Selection Mode,.,. Ctrl-c.. New, 3D Atomistic. Ctrl-v. 3D Atomistic.,. 3D Atomistic O-H, Delete. Sketch Atom H, C. 1 2 C-O 1. C-C 2 2 3, 1. Clean..

24 25: The structure of acetaldehyde. product.xsd. 3.3 LST/QST,. DMol 3. DMol3, Calculation. DMol3 Calculation. 26: DMol3 Calculation dialog, Setup tab Task Energy Geometry Optimization. Quality Medium, Functional GGA BP.

25,. Quality ( DND), orbital cutoff. Electronic., thermal smearing. Electronic. SCF Tolerance Medium, More..., DMol3 Electronic Options. SCF Use smearing,.. reactant.xsd, Run., product.xsd. product.xsd, Run.,., Project Explorer reactant DMol3 GeomOpt, product DMol3 GeomOpt 2. reactant.xsd product.xsd, reactant.outmol product.outmol..xtd.. Materials Visualizer. File Save Project, Window Close All. reactant.xsd product.xsd. 2. 3.4 DMol 3,. Tools Reaction Preview.. Window Tile Vertically.,. Tools Reaction Preview. Reaction Preview.

26 27: Reaction Preview dialog Reactant Product reactant.xsd product.xsd. Match..., Find Equivalent Atoms. Find Equivalent Atoms. 1, 6. 2xC.. 1:C 2:C.,. reactant 1:C. product 1:C.. 3D., Auto Find. Find Equivalent Atoms. Tip.,. Set Match., Auto Find.. 1,. Find Equivalent Atoms. DMol 3 LST/QST DMol 3.

27 Project Explorer ( ). Reaction Preview Number Of Frames 100. Superimpose Models. Preview,. reactant-product.xtd 3D Atomistic Trajectory. DMol 3. Animation. Bounce.,. Build Bonds, Bond Monitoring. Play. Stop. Note. reactant product.xtd,,. 3.5 LST/QST/CG, DMol 3 DMol3 Calculation. Setup Task Geometry Optimization TS Search. Quality Medium, Functional GGA BP. More..., DMol3 Transition State Search. Search protocol Complete LST/QST, Quality Medium,. Electronic. Frequency. Properties. Frequency. Job Description. Job Control Automatic, Job description TS.. Run, DMol3 Calculation. Note. LST/QST.. LST/QST, LST, QST, CG (conjugate gradient),, TS search.

28 LST/QST, TS.outmol., Project Explorer TS.outmol. Ctrl+f Energy of barrier. 14 kcal/mol, 52 kcal/mol. IR 1.,., TS.xsd., Project Explorer TS.xsd. 3D Viewer, BP/DND,. Tools Vibrational Analysis, Vibrational Analysis, Calculate.. 1988 cm 1 1., Animate.,. Vibrational Analysis. 3.6,. File Save Project, Windows Close All. Project Explorer TS DMol3 TSSearch TS.xsd. DMol3 Calculation, Setup Task TS Optimization, Run.,.,. TS Optimization.outmol,. LST/QST/CG. 1 hartree = 627.51 kcal/mol, 0.5 kcal/mol, 52 kcal/mol.,. File Save Project, Windows Close All.

29. 3.7 LST/QST Compute energy of reactants and products Determine LST maximum energy structure Refine saddle point structure using CG optimization Converged? Yes Analysis No Determine QST maximum energy structure 28: Flow chart Compute energy of reactants and products Determine LST maximum energy structure Refine saddle point structure using CG optimization Converged? Yes Analysis No Determine QST maximum energy structure 29: Step 1:

30 Compute energy of reactants and products Determine LST maximum energy structure Refine saddle point structure using CG optimization Converged? Yes Analysis No Determine QST maximum energy structure 30: Step 2: LST Compute energy of reactants and products Determine LST maximum energy structure Energy Refine saddle point structure using CG optimization 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 Reactant Path coordinate Product Converged? Yes Analysis No Determine QST maximum energy structure 31: Step 3: CG

31 Compute energy of reactants and products Determine LST maximum energy structure Energy Refine saddle point structure using CG optimization 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 Reactant Path coordinate Product Converged? Yes Analysis No Determine QST maximum energy structure 32: Step 4: QST Compute energy of reactants and products Determine LST maximum energy structure Energy Refine saddle point structure using CG optimization 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 Reactant Path coordinate Product Converged? Yes Analysis No Determine QST maximum energy structure 33: Step 5:

32 Transition Structure Transition Structure LST & QST QST LST 34: Energy surface Synchronous Transit Path LST/QST (Synchronous Transit Path) 3 4 LST r i a,b ( f ) = (1 f )rr a,b + f rp a,b (2) Object Function S ( f ) = 1 ( ra,b ra,b i ( f )) 2 ra,b i ( f + 10 6 )4 a a b ( xa x i a( f ) ) 2 (3) QST ra,b i ( f ) = (1 f )rr a,b + f rp a,b + γ(1 f ) f (4) Periodic Systems S ( f ) = 1 ( ra0,b 2 0 ra i 0,b 0 ( f ) )2 w ( ra i 0,b 0 ( f ) ) (5) a b + ra0,b R ra a,b,r( i 0,b R ( f ) )2 w ( ra i 0,b R ( f ) ) + 10 6 ( xa0 x i a 0 ( f ) ) 2 (6) a 3 T.A. Halgren and W.N. Lipscomb, Chem. Phys. Lett. 49, 225 (1977). 4 N. Govind, M. Petersen, G. Fitzerald, R.D. King-Smith, and J. Andzelm, A generalized synchronous transit method for transtion state location, Comput. Mater. Sci. 28, 250-258 (2003).

33 4 : DMol 3. : Materials Visualizer, DMol 3 :, (H), (S ), (G), (C p ). DMol 3, 0 K.,,, H, S, G, C p. DMol 3, (1- ). 5,. 1- (g) (g) H 298.15K exp = 6.40kcal/mol (7), S exp 298.15K = 9.61 kcal/mol. T = 298.15 K., G 298.15K exp = H 298.15K exp T S 298.15K exp (8) 1- (g) (g) G 298.15K exp = 9.96kcal/mol (9).,. T 1, T 0, 2.,. H T 1 rxn = T0 T 1 reactants C p dt + H T 0 rxn + T1 T 0 products C p dt (10) DMol 3,,. 5 S. Kaarsemaker and J. Coops, Rev. trav. Chim. 71, 261 (1952). H = U P V (11)

34,.,,,,. U = E tot + E vib + E trans + E rot (12) S. S = S vib + S trans + S rot (13), 3N 6(5), DMol 3.. Note., Setting Organizer. Creating a project. Tip.. Project Explorer, Online Help Project Explorer. 4.1 Materials Studio,. New Project, butene OK., butene, Project Explorer. 4.2, 1-., 3D Atomistic 2. New, 3D Atomistic Document. 2 3D Atomistic. 3D Atomistic, Sketch Atom. 4 Esc,. C-C, 2.

35,,. Adjust Hydrogen, Clean.. 3D Viewer Display Style, Display Style. Atom Ball and stick. 4,,. Measure/Change, Torsion., C-C.., 120.. 1-butene.xsd.,,. 3D Atomistic (2).xsd. Sketch Ring, 4 Member. 3D Viewer. Adjust Hydrogen, Clean 2 6. Display Style Ball and stick,.. cyclobutane.xsd. 3D Viewer Selection Mode., 3D Atomistic. 6 Clean 2, 1,.

36 35: The structure of 1-butene and cyclobutane 4.3, DMol 3. 1-butene.xsd. DMol3, Calculation. DMol3 Calculation. 36: DMol3 Calculation dialog, Setup tab Task Geometry Optimization. Quality Meidum, Funtional GGA BLYP.,. BLYP (GGA),. Electronic More..., DMol3 Electronic Options. SCF Use smearing, Smearing, 0.005,.

37,., SCF. Properties Frequency.,. (H), (S), (G), (C p ). DMol 3 0 K,,,, H, S, G, C p.,. 1-butene cyclorbutane. 1-butene.xsd, Run., cyclobutane.xsd, Run... 2. DMol 3 D 2D. 4.4 1-butene 1-butene DMol3 GeomOpt/1-butene.xsd. 1-butene.outmol.,. File Save Project, Window Close All. Project Explorer 1-butene DMol3 GeomOpt 1-butene.xsd. DMol3, Analysis, Modules DMol3 Analysis., Thermodynamic properties, 1-butene.outmol Results file. View..

38 37: The thermodynamic properties of 1-butene DMol 3. Project Explorer 1-butene DMol3 GeomOpt 1-butene.outmol. 1-butene. Ctrl+f, Properties., Entering Properties Section. Entering Properties Section Total Energy, E total 1-Butene..outmol.

39 38: Section of the DMol 3.outmol document containing the total energy in Hartree for 1-butene E total (Hartree) G 298.15 K total 1: Total and free energy of 1-butene and cyclobutane (kcal/mol) G total (Hartree) E 298.15 K T corr = E total + G total (Hartree) 1-Butene Cyclobutane Note. Hartree,. 1-butene.outmol. 1-butene.outmol, 25 K 1000 K 25 K, (,,, ). (zero-point vibrational energy, ZPVE). 1-butene 298.15 K G (kcal/mol ) 1 2..

40 39: The computed G total value at 298.15 K should be about +49 kcal/mol., G total kcal/mol Hatree (1 Hartree = 627.51 kcal/mol). 298.15 K G Hartree 1 3. 1 3, 1-butene. 1 3, 4.,.,, 1 G. G 298.15 K reaction = ( ET 298.15 K corr (cyclobutane) E 298.15 K T corr (1 butane) ) 627.51 (14) +10.23 kcal/mol, 9.96 kcal/mol.,. Note.,. DMol 3 Medium. File Save Project, Window Close All.

41 5 (Coumarin) : DMol 3. : Materials Visualizer, DMol 3 :,,. (2H-chromen-2-one).. TD-DFT, COSMO.. Note., Setting Organizer. Creating a project. Tip.. Project Explorer, Online Help Project Explorer. 5.1 Materials Studio,. New Project, DMol3 optical OK.

42, DMol3 optical, Project Explorer. 5.2. O O 40: The structure of coumarin molecule 3D Atomistic Document,., Adjust Hydrogen Clean. coumarin.xsd., COMPASS,.,,. DMol3 Calculation, Modules DMol3 Calculation, DMol3 Calculation. PBE. Setup Task Geometry Optimization, Functional GGA, PBE.,. 4.4. Electronic, Basis set DNP, Basis file 4.4.. DMole Calculation Run.,.,.,,,. File Save Project, Window Close All.

43 5.3,. coumarin.xsd. DMol3 Calculation Properties, Optics, Calculate lowest states 25. 25.. Note. Calculate Polarizability.,. Setup Task Energy. Run.,. DMol3 Analysis,. coumarin DMol3 Energy/coumarin.xsd. DMol3, DMol3 Analysis. Analysis Optics, View spectrum,. coumarin Optical Spectrum.xcd. File Save Project, Window Close All. 5.4 DMol 3 COSMO,,. COSMO,.,. coumarin.xsd. DMol3 Calculation, Setup Task Geometry Optimization. COSMO (COnductor-like Screening MOdel). Electronic, Use solvation model. More..., DMol3 Electronic Options, Solvent..

44 Solvent Water,. DMol3 Calculation Properties Optics, Run..,. courmarin DMol3 GeomOpt (2)/coumarin.xsd, DMol3 Analysis. Optics, View spectrum. 2. File Save Project, Window Close All. 2, Window Tile Vertically. 2,., 5-15 nm. (a) (b) 41: The optical spectra for (a) the coumarin molecule in vacuum and (b) in the water solvent..

45 A Materials Studio 3D Viewer 3D Viewer, Seletion, Rotation, Zoom, Translation.,. Chart Viewer..,.,. Tip.,,.